The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different cropmanagement strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy. The basis for interactions among microorganisms as communities are beginning to be elucidated, including bacteria, fungi, protists, and viruses growing on and within host organisms. Microbes interact with plants in a variety of ways: pathogens utilize the plants as a food source, symbiotic mycorrhizae and rhizobia exchange nutrients with their hosts, endophytes live inside plant cells asymptomatically and some species can provide protection to the plants against harsh environmental conditions (Rodriguez et al. 2009). Yet, basic knowledge about the structure of microbial communities across plant organs is still lacking. Wheat is a staple food globally, and is one of the most commonly grown crops, with approximately two billion bushels produced in the United States annually (USDA 2016). The fungal pathogen Fusarium graminearum has resulted in devastating yield losses, estimated at $2.491 to 7.67 billion between 1993 and 2001 (McMullen et al. 2012). There are few control options as fungicides have low efficiency against F. graminearum and there are no strongly resistant varieties (reviewed by Wegulo et al. 2015). One potential method that can contribute to an integrated approach to control is manipulation of plant microbial communities to suppress pathogen populations. The most practical method to achieve this goal involves colonization with parasitic or competitive endophytes that will kill or displace pathogens of interest. The term endophyte is used to describe microbial organisms that spend the majority or entirety of their life cycle living within a host plant (Rodriguez et al. 2009). Endophytic fungi have been documented to benefit their plant hosts in diverse conditions. They can improve salt and heat tolerance in wild grasses (Rodriguez et al. 2008). In wheat, improved germination rates have been attributed to endophytes (Hubbard et al. 2012), and protective effects of endophytes against Stagonospora infection have been documented (Sieber et al. 1988). Recently, bacterial endophytes have been shown to reduce disease and mycotoxin production by pathogens in millet (Mousa et al. 2016). Identification of wheat endophytes may provide novel strains to improve crop health and reduce disease. Previous studies of wheat microbiomes have largely focused on identifying microbes in the roots or rhizosphere (for example, Hartmann et al. 2014; Mahoney et al. 2017; Ofek et al. 2013; Yin et al. 2017), while noticeably fewer studies have focused on aboveground organs (Granzow et al. 2017; Huang et al. 2016; Karlsson et al. 2017). To our knowledge, there are no published studies which have surveyed the entire wheat microbiome, including both aboveand below-ground plant organs, with high throughput sequencing techniques. Here we classify the bacterial and fungal microbiomes of three wheat organs (stems, leaves, and roots) grown under four land management strategies (conventional tillage, no-till, low input, and organic). Microbial communities were dependent on type of plant organ, and community composition changed as plants matured. We then used the wheat microbiome analysis as the context for identifying and testing potential biocontrol strains isolated from the experimental plots for protective abilities against F. graminearum seedling damping-off. Corresponding author: F. Trail; E-mail: [email protected] *The e-Xtra logo stands for “electronic extra” and indicates that 13 supplementary figures and 8 supplementary tables are published online. © 2017 The American Phytopathological Society